Mon Oct 10 14:25:11 PDT 2011 #!/bin/csh -f # input: # $1 receptor coordinates file; # $2 grid size; # $3 # of iterations for the first run; # $4 # of iterations for the second run; # $5 # of iterations for the third run; # output: # delphi map: $1.phi # log file: delphi.out set RECCRG = rec+sph2.crg set GRID = 179 set n1 = 50 set n2 = 120 set n3 = 180 set DELPHI = $DOCK_BASE/private/delphi set VDW = vdw.siz #set VDW = vdw.hydren set CRG = amb2.crg.oxt set PRM = genric.prm # three step focussing calc. if (-e ARCDAT) /bin/rm ARCDAT cp $VDW fort.11 cp $CRG fort.12 cp $RECCRG fort.13 echo "gsize=$GRID, perfil=20, bndcon=2, linit=$n1\n" >! fort.10 cat $PRM >> fort.10 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=60, bndcon=3, linit=$n2\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=90, bndcon=3, linit=$n3\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) /bin/rm fort.1[0-3] fort.18 ARCDAT mv fort.14 $RECCRG:r.phi ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Mon Oct 10 2011 at 14:25:12 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 317 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2576 !!! WARNING: SEP 323 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.6110119 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : dipolar x,y,z periodic bc. flags : F F F # of linear iterations : 50 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 20.00000 xmin,xmax (A): -7.914000 44.05300 ymin,ymax (A): 12.97400 71.23800 zmin,zma (A): 55.66400 107.6440 x,y,z range (A): 51.96700 58.26400 51.98000 scale (grids/A): 0.6110119 object centre (A): 18.06950 42.10600 81.65400 number of atom coordinates read : 2576 total number of charged atoms : 2415 net assigned charge : -2.474988 assigned positive charge : 381.6219 centred at (gu) : 90.10313 90.79818 89.65573 assigned negative charge : -384.0974 centred at (gu) : 89.88145 90.68415 89.67679 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6453 nv = 96 ne = 84 npr = 51434 no. pairs analyzed = 51434 no. exposed pairs = 3548 no. arc points = 25164 no. surface atoms = 1190 nbur = 1386 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 316 mr = 3206 m= 1 mr = 14 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3000000 number of dielectric boundary points 3550 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2452 ## 255 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 7877 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.3231841E-10 -2.4329450E-09 midg,1,midg; midg,igrid,midg -6.1807102E-09 4.9672333E-09 1,midg,midg; igrid,midg,midg -1.2738322E-08 9.5804733E-09 gauss-seidel spectral radius is 0.9861370 estimated iterations to convergence 70 setup time was (sec) 0.5400000 now iterating at: 14:25:12 rms-change max change #iterations 0.1131944 17.01385 at 10iterations 9.9581238E-03 1.696875 at 20iterations 8.7627571E-04 0.1387787 at 30iterations 7.8842408E-05 1.2393951E-02 at 40iterations 7.0927217E-06 9.3746185E-04 at 50iterations finished qdiffx linear iterations at : 14:25:15 total time elapsed so far: 3.420000 # loops : 50 mean,max change (kT/e) : 7.0927217E-06 9.3746185E-04 energy calculations done at 3.420000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.630000 DelPhi exited at 14:25:16 3.630u 0.212s 0:04.41 87.0% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Mon Oct 10 2011 at 14:25:16 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 317 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2576 !!! WARNING: SEP 323 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.833036 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 120 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 60.00000 xmin,xmax (A): -7.914000 44.05300 ymin,ymax (A): 12.97400 71.23800 zmin,zma (A): 55.66400 107.6440 x,y,z range (A): 51.96700 58.26400 51.98000 scale (grids/A): 1.833036 object centre (A): 18.06950 42.10600 81.65400 number of atom coordinates read : 2576 total number of charged atoms : 2415 net assigned charge : -2.474988 assigned positive charge : 381.6219 centred at (gu) : 90.30871 92.39414 88.96676 assigned negative charge : -384.0974 centred at (gu) : 89.64411 92.05213 89.03007 start vw surface at 0.1700000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 69404 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25164 grid for indexing accessible points = 1.400000 m= 22668 mr = 45523 m= 2969 mr = 15485 m= 141 mr = 1467 m= 2 mr = 26 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5500000 number of dielectric boundary points 32683 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 186 iepsmp to db, and charging done at 0.6800000 number of grid points assigned charge 18931 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 0.6110119 object centre at (A) : 18.06950 42.10600 81.65400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.2548123E-02 2.7163797E-03 midg,1,midg; midg,igrid,midg -4.9673086E-03 4.2244191E-03 1,midg,midg; igrid,midg,midg -3.4052990E-02 3.0823988E-03 gauss-seidel spectral radius is 0.9985340 estimated iterations to convergence 207 setup time was (sec) 0.8600000 now iterating at: 14:25:17 rms-change max change #iterations 3.928721 167.9518 at 10iterations 1.775063 64.85808 at 20iterations 0.8070853 27.67145 at 30iterations 0.3671817 12.53960 at 40iterations 0.1667735 5.818484 at 50iterations 7.5880371E-02 2.577250 at 60iterations 3.4539025E-02 1.255552 at 70iterations 1.5683539E-02 0.5288887 at 80iterations 7.1499040E-03 0.2863746 at 90iterations 3.2486855E-03 0.1174507 at 100iterations 1.4754534E-03 5.4376602E-02 at 110iterations 6.7524589E-04 2.4734497E-02 at 120iterations finished qdiffx linear iterations at : 14:25:24 total time elapsed so far: 7.800000 # loops : 120 mean,max change (kT/e) : 6.7524589E-04 2.4734497E-02 energy calculations done at 7.800000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.000000 DelPhi exited at 14:25:25 8.000u 0.215s 0:08.70 94.3% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Mon Oct 10 2011 at 14:25:25 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 317 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2576 !!! WARNING: SEP 323 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.749554 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 180 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 90.00000 xmin,xmax (A): -7.914000 44.05300 ymin,ymax (A): 12.97400 71.23800 zmin,zma (A): 55.66400 107.6440 x,y,z range (A): 51.96700 58.26400 51.98000 scale (grids/A): 2.749554 object centre (A): 18.06950 42.10600 81.65400 number of atom coordinates read : 2576 total number of charged atoms : 2415 net assigned charge : -2.474988 assigned positive charge : 381.6219 centred at (gu) : 90.46306 93.59102 88.44989 assigned negative charge : -384.0974 centred at (gu) : 89.46600 93.07809 88.54511 start vw surface at 0.1500000 fill in re-entrant regions at 0.4500000 boundary points on vw surface= 160663 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25164 grid for indexing accessible points = 1.400000 m= 75359 mr = 111564 m= 24607 mr = 58856 m= 4851 mr = 18500 m= 545 mr = 3113 m= 41 mr = 269 m= 1 mr = 15 m= 0 mr = 0 time to grow re-entrant surface = 0.7499999 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.330000 number of dielectric boundary points 73750 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.470000 number of grid points assigned charge 19315 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 1.833036 object centre at (A) : 18.06950 42.10600 81.65400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2582965 6.5245703E-02 midg,1,midg; midg,igrid,midg -2.7304508E-02 -5.2349027E-02 1,midg,midg; igrid,midg,midg -0.3558597 -3.5085008E-02 gauss-seidel spectral radius is 0.9992395 estimated iterations to convergence 286 setup time was (sec) 1.660000 now iterating at: 14:25:27 rms-change max change #iterations 9.537141 325.5494 at 10iterations 5.587192 157.3997 at 20iterations 3.248449 75.20779 at 30iterations 1.877368 41.95695 at 40iterations 1.083263 23.00354 at 50iterations 0.6228022 13.31524 at 60iterations 0.3568113 7.762951 at 70iterations 0.2044866 4.370321 at 80iterations 0.1170459 2.371356 at 90iterations 6.6853963E-02 1.302650 at 100iterations 3.8240366E-02 0.8442512 at 110iterations 2.1807121E-02 0.4428349 at 120iterations 1.2454622E-02 0.2497663 at 130iterations 7.1030357E-03 0.1523018 at 140iterations 4.0557659E-03 7.5485229E-02 at 150iterations 2.3126358E-03 4.9004555E-02 at 160iterations 1.3181723E-03 2.6896954E-02 at 170iterations 7.5196958E-04 1.5716076E-02 at 180iterations finished qdiffx linear iterations at : 14:25:38 total time elapsed so far: 12.70000 # loops : 180 mean,max change (kT/e) : 7.5196958E-04 1.5716076E-02 energy calculations done at 12.70000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.89000 DelPhi exited at 14:25:38 12.893u 0.237s 0:13.46 97.4% 0+0k 0+0io 0pf+0w